GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Acidovorax sp. GW101-3H11

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3326
          Length = 260

 Score =  105 bits (261), Expect = 2e-27
 Identities = 79/246 (32%), Positives = 120/246 (48%), Gaps = 16/246 (6%)

Query: 142 NAILLFAV-LPVIAFWLLHGGFGLEVVETPLWG-------GLMVTLVLSFVGIAVSLPVG 193
           NA L+ AV L V+A  LL  G  L  +  P+         G   TL L+ +  +V L +G
Sbjct: 17  NATLVSAVILMVLALALL--GQLLSFLPEPIGSNAQAFSDGARTTLWLTLISGSVGLVLG 74

Query: 194 ILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLLRALIG 253
              AL R +R  V+R     +I VIRG PL+  +      LP+ +P G N+     A++ 
Sbjct: 75  TGAALARTARWAVVRWAASFYIWVIRGTPLLVQILFVYFALPVLVP-GLNLPDFAAAVLA 133

Query: 254 VSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFI 313
           + +   AY AE IR GL A+P+GQ E A +LGLG       ++ PQA K+ +P +V+ F+
Sbjct: 134 LGLNVGAYNAEAIRAGLLAVPRGQTEAAKALGLGRMHVFFDVVFPQAFKISLPPLVSNFV 193

Query: 314 GTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGF 373
              KD+SL   IG+ +L      N  +   ++   PI  L      + L    +++ S  
Sbjct: 194 ALLKDSSLAYAIGVVEL-----TNVGNRIQSATFQPIATLSTVAITYLLLTTLVTQISNA 248

Query: 374 MERHLD 379
           +E   D
Sbjct: 249 VEYRFD 254



 Score = 30.4 bits (67), Expect = 6e-05
 Identities = 39/139 (28%), Positives = 57/139 (41%), Gaps = 20/139 (14%)

Query: 41  VILTILALALIAWAVPHLVNWLF--IQAVWSGPDRTFCATTLQGGIQPDGWSGAC----- 93
           VIL +LALAL+   +  L   +    QA   G   T   T + G +     +GA      
Sbjct: 24  VILMVLALALLGQLLSFLPEPIGSNAQAFSDGARTTLWLTLISGSVGLVLGTGAALARTA 83

Query: 94  -WAFISAKYDQFIFGRYPLGERWRPAIVGILFILLLVPMLIPSAPRKGLNAILLFAVLPV 152
            WA +      +I+       R  P +V ILF+   +P+L+P     GLN  L      V
Sbjct: 84  RWAVVRWAASFYIWVI-----RGTPLLVQILFVYFALPVLVP-----GLN--LPDFAAAV 131

Query: 153 IAFWLLHGGFGLEVVETPL 171
           +A  L  G +  E +   L
Sbjct: 132 LALGLNVGAYNAEAIRAGL 150


Lambda     K      H
   0.330    0.145    0.469 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 259
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 384
Length of database: 260
Length adjustment: 27
Effective length of query: 357
Effective length of database: 233
Effective search space:    83181
Effective search space used:    83181
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory